gem install nokogiri -v '1.6.8.1' fails

Question

Building a new Rails app and getting a problem with nokogiri. Said to try gem install nokogiri -v '1.6.8.1' which fails with output below. I tried deleting Gemfile.lock and using the Gemfile from another app which has no problem—bundle install still fails. The original failure is bundle install which continues to work in other apps.

From console:

gem install nokogiri -v '1.6.8.1'
Building native extensions.  This could take a while...
ERROR:  Error installing nokogiri:
    ERROR: Failed to build gem native extension.

    current directory: ~/.gem/ruby/2.3.1/gems/nokogiri-1.6.8.1/ext/nokogiri
~/.rubies/ruby-2.3.1/bin/ruby -r ./siteconf20161008-60071-tmqi2l.rb extconf.rb
Ignoring byebug-6.0.2 because its extensions are not built.  Try: gem pristine byebug --version 6.0.2
Ignoring byebug-3.4.0 because its extensions are not built.  Try: gem pristine byebug --version 3.4.0
checking if the C compiler accepts ... yes
checking if the C compiler accepts -Wno-error=unused-command-line-argument-hard-error-in-future... no
Building nokogiri using packaged libraries.
Using mini_portile version 2.1.0
checking for iconv.h... yes
checking for gzdopen() in -lz... yes
checking for iconv using --with-opt-* flags... yes
************************************************************************
IMPORTANT NOTICE:

Building Nokogiri with a packaged version of libxml2-2.9.4.

Team Nokogiri will keep on doing their best to provide security
updates in a timely manner, but if this is a concern for you and want
to use the system library instead; abort this installation process and
reinstall nokogiri as follows:

    gem install nokogiri -- --use-system-libraries
        [--with-xml2-config=/path/to/xml2-config]
        [--with-xslt-config=/path/to/xslt-config]

If you are using Bundler, tell it to use the option:

    bundle config build.nokogiri --use-system-libraries
    bundle install

Note, however, that nokogiri is not fully compatible with arbitrary
versions of libxml2 provided by OS/package vendors.
************************************************************************
Extracting libxml2-2.9.4.tar.gz into tmp/x86_64-apple-darwin16.1.0/ports/libxml2/2.9.4... OK
Running 'configure' for libxml2 2.9.4... OK
Running 'compile' for libxml2 2.9.4... ERROR, review '~/.gem/ruby/2.3.1/gems/nokogiri-1.6.8.1/ext/nokogiri/tmp/x86_64-apple-darwin16.1.0/ports/libxml2/2.9.4/compile.log' to see what happened. Last lines are:
========================================================================
    unsigned short* in = (unsigned short*) inb;
                         ^~~~~~~~~~~~~~~~~~~~~
encoding.c:815:27: warning: cast from 'unsigned char *' to 'unsigned short *' increases required alignment from 1 to 2 [-Wcast-align]
    unsigned short* out = (unsigned short*) outb;
                          ^~~~~~~~~~~~~~~~~~~~~~
4 warnings generated.
  CC       error.lo
  CC       parserInternals.lo
  CC       parser.lo
  CC       tree.lo
  CC       hash.lo
  CC       list.lo
  CC       xmlIO.lo
xmlIO.c:1450:52: error: use of undeclared identifier 'LZMA_OK'
    ret =  (__libxml2_xzclose((xzFile) context) == LZMA_OK ) ? 0 : -1;
                                                   ^
1 error generated.
make[2]: *** [xmlIO.lo] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
========================================================================
*** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers.  Check the mkmf.log file for more details.  You may
need configuration options.

Provided configuration options:
    --with-opt-dir
    --with-opt-include
    --without-opt-include=${opt-dir}/include
    --with-opt-lib
    --without-opt-lib=${opt-dir}/lib
    --with-make-prog
    --without-make-prog
    --srcdir=.
    --curdir
    --ruby=~/.rubies/ruby-2.3.1/bin/$(RUBY_BASE_NAME)
    --help
    --clean
    --use-system-libraries
    --enable-static
    --disable-static
    --with-zlib-dir
    --without-zlib-dir
    --with-zlib-include
    --without-zlib-include=${zlib-dir}/include
    --with-zlib-lib
    --without-zlib-lib=${zlib-dir}/lib
    --enable-cross-build
    --disable-cross-build
~/.rubies/ruby-2.3.1/lib/ruby/gems/2.3.0/gems/mini_portile2-2.1.0/lib/mini_portile2/mini_portile.rb:366:in `block in execute': Failed to complete compile task (RuntimeError)
    from ~/.rubies/ruby-2.3.1/lib/ruby/gems/2.3.0/gems/mini_portile2-2.1.0/lib/mini_portile2/mini_portile.rb:337:in `chdir'
    from ~/.rubies/ruby-2.3.1/lib/ruby/gems/2.3.0/gems/mini_portile2-2.1.0/lib/mini_portile2/mini_portile.rb:337:in `execute'
    from ~/.rubies/ruby-2.3.1/lib/ruby/gems/2.3.0/gems/mini_portile2-2.1.0/lib/mini_portile2/mini_portile.rb:111:in `compile'
    from ~/.rubies/ruby-2.3.1/lib/ruby/gems/2.3.0/gems/mini_portile2-2.1.0/lib/mini_portile2/mini_portile.rb:150:in `cook'
    from extconf.rb:365:in `block (2 levels) in process_recipe'
    from extconf.rb:258:in `block in chdir_for_build'
    from extconf.rb:257:in `chdir'
    from extconf.rb:257:in `chdir_for_build'
    from extconf.rb:364:in `block in process_recipe'
    from extconf.rb:263:in `tap'
    from extconf.rb:263:in `process_recipe'
    from extconf.rb:556:in `<main>'

To see why this extension failed to compile, please check the mkmf.log which can be found here:

  ~/.gem/ruby/2.3.1/extensions/x86_64-darwin-16/2.3.0-static/nokogiri-1.6.8.1/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in ~/.gem/ruby/2.3.1/gems/nokogiri-1.6.8.1 for inspection.
Results logged to ~/.gem/ruby/2.3.1/extensions/x86_64-darwin-16/2.3.0-static/nokogiri-1.6.8.1/gem_make.out

mkmf.log:

"clang -o conftest -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin16 -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0 -I.  -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -I/usr/local/opt/libyaml/include -I/usr/local/opt/gdbm/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -pipe  conftest.c  -L. -L~/.rubies/ruby-2.3.1/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/gdbm/lib -L. -fstack-protector -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/gdbm/lib     -lruby-static -framework CoreFoundation  -lpthread -ldl -lobjc  "
checked program was:
/* begin */
1: #include "ruby.h"
2: 
3: int main(int argc, char **argv)
4: {
5:   return 0;
6: }
/* end */

"clang -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin16 -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0 -I.  -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -I/usr/local/opt/libyaml/include -I/usr/local/opt/gdbm/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -pipe    -Werror -c conftest.c"
checked program was:
/* begin */
1: #include "ruby.h"
2: 
3: int main() {return 0;}
/* end */

"clang -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin16 -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0 -I.  -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -I/usr/local/opt/libyaml/include -I/usr/local/opt/gdbm/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -pipe  -Wno-error=unused-command-line-argument-hard-error-in-future   -Werror -c conftest.c"
error: unknown warning option '-Werror=unused-command-line-argument-hard-error-in-future'; did you mean '-Werror=unused-command-line-argument'? [-Werror,-Wunknown-warning-option]
checked program was:
/* begin */
1: #include "ruby.h"
2: 
3: int main() {return 0;}
/* end */

have_header: checking for iconv.h... -------------------- yes

"clang -E -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin16 -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0 -I.  -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -I/usr/local/opt/libyaml/include -I/usr/local/opt/gdbm/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -pipe   conftest.c -o conftest.i"
checked program was:
/* begin */
1: #include "ruby.h"
2: 
3: #include <iconv.h>
/* end */

--------------------

have_library: checking for gzdopen() in -lz... -------------------- yes

"clang -o conftest -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin16 -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0 -I.  -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -I/usr/local/opt/libyaml/include -I/usr/local/opt/gdbm/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -pipe  conftest.c  -L. -L~/.rubies/ruby-2.3.1/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/gdbm/lib -L. -fstack-protector -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/gdbm/lib     -lruby-static -framework CoreFoundation -lz  -lpthread -ldl -lobjc  "
checked program was:
/* begin */
 1: #include "ruby.h"
 2: 
 3: #include <zlib.h>
 4: 
 5: /*top*/
 6: extern int t(void);
 7: int main(int argc, char **argv)
 8: {
 9:   if (argc > 1000000) {
10:     printf("%p", &t);
11:   }
12: 
13:   return 0;
14: }
15: int t(void) { void ((*volatile p)()); p = (void ((*)()))gzdopen; return !p; }
/* end */

--------------------

have_iconv?: checking for iconv using --with-opt-* flags... -------------------- yes

"clang -o conftest -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin16 -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0 -I.  -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -I/usr/local/opt/libyaml/include -I/usr/local/opt/gdbm/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -pipe  conftest.c  -L. -L~/.rubies/ruby-2.3.1/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/gdbm/lib -L. -fstack-protector -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/gdbm/lib     -lruby-static -framework CoreFoundation  -lpthread -ldl -lobjc  "
Undefined symbols for architecture x86_64:
  "_iconv", referenced from:
      _main in conftest-d46614.o
  "_iconv_open", referenced from:
      _main in conftest-d46614.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
checked program was:
/* begin */
 1: #include "ruby.h"
 2: 
 3: #include <stdlib.h>
 4: #include <iconv.h>
 5: 
 6: int main(void)
 7: {
 8:     iconv_t cd = iconv_open("", "");
 9:     iconv(cd, NULL, NULL, NULL, NULL);
10:     return EXIT_SUCCESS;
11: }
/* end */

"clang -o conftest -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin16 -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0 -I.  -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -I/usr/local/opt/libyaml/include -I/usr/local/opt/gdbm/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -pipe  conftest.c  -L. -L~/.rubies/ruby-2.3.1/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/gdbm/lib -L. -fstack-protector -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/gdbm/lib     -lruby-static -framework CoreFoundation -liconv -lpthread -ldl -lobjc  "
checked program was:
/* begin */
 1: #include "ruby.h"
 2: 
 3: #include <stdlib.h>
 4: #include <iconv.h>
 5: 
 6: int main(void)
 7: {
 8:     iconv_t cd = iconv_open("", "");
 9:     iconv(cd, NULL, NULL, NULL, NULL);
10:     return EXIT_SUCCESS;
11: }
/* end */

--------------------

gem_make.out:

current directory: ~/.gem/ruby/2.3.1/gems/nokogiri-1.6.8.1/ext/nokogiri
~/.rubies/ruby-2.3.1/bin/ruby -r ./siteconf20161008-60071-tmqi2l.rb extconf.rb
Ignoring byebug-6.0.2 because its extensions are not built.  Try: gem pristine byebug --version 6.0.2
Ignoring byebug-3.4.0 because its extensions are not built.  Try: gem pristine byebug --version 3.4.0
checking if the C compiler accepts ... yes
checking if the C compiler accepts -Wno-error=unused-command-line-argument-hard-error-in-future... no
Building nokogiri using packaged libraries.
Using mini_portile version 2.1.0
checking for iconv.h... yes
checking for gzdopen() in -lz... yes
checking for iconv using --with-opt-* flags... yes
************************************************************************
IMPORTANT NOTICE:

Building Nokogiri with a packaged version of libxml2-2.9.4.

Team Nokogiri will keep on doing their best to provide security
updates in a timely manner, but if this is a concern for you and want
to use the system library instead; abort this installation process and
reinstall nokogiri as follows:

    gem install nokogiri -- --use-system-libraries
        [--with-xml2-config=/path/to/xml2-config]
        [--with-xslt-config=/path/to/xslt-config]

If you are using Bundler, tell it to use the option:

    bundle config build.nokogiri --use-system-libraries
    bundle install

Note, however, that nokogiri is not fully compatible with arbitrary
versions of libxml2 provided by OS/package vendors.
************************************************************************
Extracting libxml2-2.9.4.tar.gz into tmp/x86_64-apple-darwin16.1.0/ports/libxml2/2.9.4... OK
Running 'configure' for libxml2 2.9.4... OK
Running 'compile' for libxml2 2.9.4... ERROR, review '~/.gem/ruby/2.3.1/gems/nokogiri-1.6.8.1/ext/nokogiri/tmp/x86_64-apple-darwin16.1.0/ports/libxml2/2.9.4/compile.log' to see what happened. Last lines are:
========================================================================
    unsigned short* in = (unsigned short*) inb;
                         ^~~~~~~~~~~~~~~~~~~~~
encoding.c:815:27: warning: cast from 'unsigned char *' to 'unsigned short *' increases required alignment from 1 to 2 [-Wcast-align]
    unsigned short* out = (unsigned short*) outb;
                          ^~~~~~~~~~~~~~~~~~~~~~
4 warnings generated.
  CC       error.lo
  CC       parserInternals.lo
  CC       parser.lo
  CC       tree.lo
  CC       hash.lo
  CC       list.lo
  CC       xmlIO.lo
xmlIO.c:1450:52: error: use of undeclared identifier 'LZMA_OK'
    ret =  (__libxml2_xzclose((xzFile) context) == LZMA_OK ) ? 0 : -1;
                                                   ^
1 error generated.
make[2]: *** [xmlIO.lo] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
========================================================================
*** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers.  Check the mkmf.log file for more details.  You may
need configuration options.

Provided configuration options:
    --with-opt-dir
    --with-opt-include
    --without-opt-include=${opt-dir}/include
    --with-opt-lib
    --without-opt-lib=${opt-dir}/lib
    --with-make-prog
    --without-make-prog
    --srcdir=.
    --curdir
    --ruby=~/.rubies/ruby-2.3.1/bin/$(RUBY_BASE_NAME)
    --help
    --clean
    --use-system-libraries
    --enable-static
    --disable-static
    --with-zlib-dir
    --without-zlib-dir
    --with-zlib-include
    --without-zlib-include=${zlib-dir}/include
    --with-zlib-lib
    --without-zlib-lib=${zlib-dir}/lib
    --enable-cross-build
    --disable-cross-build
~/.rubies/ruby-2.3.1/lib/ruby/gems/2.3.0/gems/mini_portile2-2.1.0/lib/mini_portile2/mini_portile.rb:366:in `block in execute': Failed to complete compile task (RuntimeError)
    from ~/.rubies/ruby-2.3.1/lib/ruby/gems/2.3.0/gems/mini_portile2-2.1.0/lib/mini_portile2/mini_portile.rb:337:in `chdir'
    from ~/.rubies/ruby-2.3.1/lib/ruby/gems/2.3.0/gems/mini_portile2-2.1.0/lib/mini_portile2/mini_portile.rb:337:in `execute'
    from ~/.rubies/ruby-2.3.1/lib/ruby/gems/2.3.0/gems/mini_portile2-2.1.0/lib/mini_portile2/mini_portile.rb:111:in `compile'
    from ~/.rubies/ruby-2.3.1/lib/ruby/gems/2.3.0/gems/mini_portile2-2.1.0/lib/mini_portile2/mini_portile.rb:150:in `cook'
    from extconf.rb:365:in `block (2 levels) in process_recipe'
    from extconf.rb:258:in `block in chdir_for_build'
    from extconf.rb:257:in `chdir'
    from extconf.rb:257:in `chdir_for_build'
    from extconf.rb:364:in `block in process_recipe'
    from extconf.rb:263:in `tap'
    from extconf.rb:263:in `process_recipe'
    from extconf.rb:556:in `<main>'

To see why this extension failed to compile, please check the mkmf.log which can be found here:

  ~/.gem/ruby/2.3.1/extensions/x86_64-darwin-16/2.3.0-static/nokogiri-1.6.8.1/mkmf.log

extconf failed, exit code 1

Answer 1

Run this first:

xcode-select --install

Then rerun your bundle install

Reference: https://github.com/sparklemotion/nokogiri/issues/1483

Answer 2

I tried @the_basterd's recommendation. That didn't work, but the reference was good—thank you the_basterd. What worked from that reference was:

brew install libxml2

bundle config build.nokogiri --use-system-libraries --with-xml2-include=/usr/local/opt/libxml2/include/libxml2

Reference: https://github.com/sparklemotion/nokogiri/issues/1483

Later postings at that ref said that what I posted above "is strongly recommended against by the Nokogiri."

brew unlink xz; bundle install; brew link xz is preferred.